TFBS::PatternGen::SimplePFM(3pm)			User Contributed Perl Documentation			  TFBS::PatternGen::SimplePFM(3pm)

NAME

       TFBS::PatternGen::SimplePFM - a simple position frequency matrix factory

SYNOPSIS

	   my @sequences = qw( AAGCCT AGGCAT AAGCCT
			       AAGCCT AGGCAT AGGCCT
			       AGGCAT AGGTTT AGGCAT
			       AGGCCT AGGCCT );
	   my $patterngen =
		   TFBS::PatternGen::SimplePFM->new(-seq_list=>@sequences);

	   my $pfm = $patterngen->pattern(); # $pfm is now a TFBS::Matrix::PFM object

DESCRIPTION

       TFBS::PatternGen::SimplePFM generates a position frequency matrix from a set of nucleotide sequences of equal length, The sequences can be
       passed either as strings, as Bio::Seq objects or as a fasta file.

       This pattern generator always creates only one pattern from a given set of sequences.

   new
	Title	: new
	Usage	: my $db = TFBS::PatternGen::SimplePFM->new(%args);
	Function: the constructor for the TFBS::PatternGen::SimplePFM
		   object
	Returns : a TFBS::PatternGen::SimplePFM obkect
	Args	: This method takes named arguments;
		   you must specify one of the following
		   -seq_list	 # a reference to an array of strings
				 # and/or Bio::Seq objects
		     # or
		   -seq_stream	 # A Bio::SeqIO object
		     # or
		   -seq_file	 # the name of the fasta file containing
				 # all the sequences

   pattern
   all_patterns
   patternSet
       The three above methods are used fro the retrieval of patterns, and are common to all TFBS::PatternGen::* classes. Please see
       TFBS::PatternGen for details.

perl v5.14.2							    2008-01-24					  TFBS::PatternGen::SimplePFM(3pm)